Article abstract

Nature Methods 6, 377 - 382 (2009)
Published online: 6 April 2009 | Corrected online: 19 April 2009 | doi:10.1038/nmeth.1315

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang1,3, Catalin Barbacioru2,3, Yangzhou Wang2, Ellen Nordman2, Clarence Lee2, Nanlan Xu2, Xiaohui Wang2, John Bodeau2, Brian B Tuch2, Asim Siddiqui2, Kaiqin Lao2 & M Azim Surani1

Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression profiling assay. Using our mRNA-Seq assay with only a single mouse blastomere, we detected the expression of 75% (5,270) more genes than microarray techniques and identified 1,753 previously unknown splice junctions called by at least 5 reads. Moreover, 8–19% of the genes with multiple known transcript isoforms expressed at least two isoforms in the same blastomere or oocyte, which unambiguously demonstrated the complexity of the transcript variants at whole-genome scale in individual cells. Finally, for Dicer1-/- and Ago2-/- (Eif2c2-/-) oocytes, we found that 1,696 and 1,553 genes, respectively, were abnormally upregulated compared to wild-type controls, with 619 genes in common.

Top
  1. Wellcome Trust–Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK.
  2. Molecular Cell Biology Division, Applied Biosystems, Foster City, California, USA.
  3. These authors contributed equally to this work.

Correspondence to: M Azim Surani1 e-mail: as10021@mole.bio.cam.ac.uk

Correspondence to: Kaiqin Lao2 e-mail: laokq@appliedbiosystems.com

* In the version of this article initially published online, Figure 2d was a duplicate of Figure 2c. The error has been corrected for the print, PDF and HTML versions of this article.

MORE ARTICLES LIKE THIS

These links to content published by NPG are automatically generated.

NEWS AND VIEWS

The beginning of the end for microarrays?

Nature Methods News and Views (01 Jul 2008)

Molecular biology Power sequencing

Nature News and Views (26 Jun 2008)

See all 3 matches for News And Views

RESEARCH

Alternative isoform regulation in human tissue transcriptomes

Nature Article (27 Nov 2008)

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

Nature Genetics Brief Communication (01 Dec 2008)

See all 22 matches for Research

Extra navigation

Apply for your free subscription to
Nature Methods

Subscribe

Search PubMed for

Open Innovation Challenges

naturejobs

More science jobs
Post a job for free

ADVERTISEMENT